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IMPROVE

Libraries and scripts for basic IMPROVE functionalities

Example

This example shows how to the use the improve library with the GraphDRP model.

GraphDRP

Clone the model into some directory. E.g., /lambda_stor/data/apartin/projects/IMPROVE/pan-models

cd /lambda_stor/data/apartin/projects/IMPROVE/pan-models
git clone https://github.com/JDACS4C-IMPROVE/GraphDRP
cd GraphDRP
git checkout cristina/candleize-ap

Download data

Download the cross-study analysis (CSA) benchmark data into the model directory from https://web.cels.anl.gov/projects/IMPROVE_FTP/candle/public/improve/benchmarks/single_drug_drp/benchmark-data-pilot1/

wget --cut-dirs=7 -P ./ -nH -np -m ftp://ftp.mcs.anl.gov/pub/candle/public/improve/benchmarks/single_drug_drp/benchmark-data-pilot1/csa_data

Environment

  1. clone the improve repo to a directory of your preference. For example:
cd ..
git clone https://github.com/JDACS4C-IMPROVE/IMPROVE
git checkout develop

As a result of the commands above, the IMPROVE repo will be loacted in /lambda_stor/data/apartin/projects/IMPROVE/pan-models/IMPROVE

  1. cd to the model repo.
cd /lambda_stor/data/apartin/projects/IMPROVE/pan-models/GraphDRP
  1. specify $PYTHOPATH and $IMPROVE_DATA_DIR environment variables.
export PYTHONPATH=$PYTHONPATH:/lambda_stor/data/apartin/projects/IMPROVE/pan-models/IMPROVE
export IMPROVE_DATA_DIR="./csa_data/"

Packages

TODO

Utils

TODO

  • name: utils.py